MmuINT0117070 @ mm10
Intron Retention
Gene
ENSMUSG00000029491 | Pde6b
Description
phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide [Source:MGI Symbol;Acc:MGI:97525]
Coordinates
chr5:108423008-108423583:+
Coord C1 exon
chr5:108423008-108423157
Coord A exon
chr5:108423158-108423439
Coord C2 exon
chr5:108423440-108423583
Length
282 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
ACACTCCTGTCTACCTCCAGTCT
3' ss Score
8.61
Exon sequences
Seq C1 exon
GAGGGGCCCCTGGATGATTCAGGATGGGTGATCAAGAATGTCCTCTCTATGCCCATTGTCAACAAGAAAGAGGAGATTGTGGGGGTGGCAACCTTCTACAACAGGAAAGATGGAAAGCCCTTCGATGATCAAGATGAAGTCCTTATGGAG
Seq A exon
GTAAATATCTAGTATCATACATGGACAAAAGGGTCCATCTATCATGTCGTGGGATATCAGTGAGGACTGTCCCTCTCCACACATATTTGGACCCTGATTAGCACTACATCAGGGAGAAGGGGACAAAGATAGTTCCCAAAGTTCTATCTTGGGAGACCCATTCATAGACATCCACTGTACTGTAGCAGTCTGGGAAACTGGCCTCTGAGACACCGGTATAAAACGTAGTTAAAACTCACCAAAGTGCATGGCTAATGGGGCGACACTCCTGTCTACCTCCAG
Seq C2 exon
TCTCTGACACAGTTCCTGGGGTGGTCAGTGCTGAACACAGACACCTATGACAAGATGAACAAGCTGGAGAACCGTAAGGACATCGCCCAGGACATGGTTCTGTACCATGTGAGATGTGACAAAGATGAAATCCAGGAAATCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029491:ENSMUST00000031456:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0159021=GAF=FE(27.5=100)
A:
NA
C2:
PF0159021=GAF=PD(5.1=18.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGGGCCCCTGGATGATTC
R:
AGGATTTCCTGGATTTCATCTTTGT
Band lengths:
292-574
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types